So it's been a few years (lol) since my earlier post on this subject, and my system's changed. When I'm working on a pattern, I keep all the bobbins for that pattern together in numerical order on one or more rings, with all the rings together in a ziploc bag. Then I make myself a folding card with punched holes along the edges, marked with the numbers and symbols for each colour. (It's folded in such a way that the floss is on the interior when the card is closed up.)

As I work, I cut chunks of floss off the bobbins and ring knot them onto the appropriate hole in the card. This has been the most practical system I've found so far.

I keep my floss in those plastic boxes you can get at Michaels. I have two smaller Darice boxes with 7 compartments, and I use those to hold floss for specific projects.

So I don't lose track of what floss I have, I have a printed checklist of all the DMC colours, so I make sure to add a check every time I get a new one, erase the check when I finish one etc, so I don't have to get out the boxes to see if I have everything I need.